Posted by Web Master (December 13, 2016)

Release of Mascot Server 2.6

We are pleased to announce the release of Mascot Server 2.6. Details of the new features can be found here.

Posted by Web Master (November 25, 2016)

Mascot Server 2.6 preview

This website is now running the Mascot Server 2.6 release candidate, exposing it to thousands of searches each day. This page highlights important new features.

If you spot any bugs or experience any problems, please email with details. Now matter how much testing we do ourselves, there will always be some bugs that we miss. The more we catch in the next few days, the sooner we can make a release.

Posted by Web Master (September 30, 2016)

NCBInr is dead, long live NCBIprot

NCBI recently dropped gi number identifiers, as explained in this blog article. This change breaks the old database definition, NCBInr, so we have created a new definition for accession.version identifiers, NCBIprot; now available on this site. If you search nr on your in-house Mascot Server, you’ll want to review the NCBI nr database setup page.

The strengths of nr are that it is comprehensive and frequently updated. The downside is that it is a huge database. As of September 2016, the 54 GB Fasta file contained 94 million entries. Even with a tight taxonomy filter, the size of the search space means that it is harder to get a significant match than in a database like SwissProt. If you have an in-house Mascot Server, there will usually be a better choice of database, such as a Uniprot complete proteome for your organism of interest.

Posted by Web Master (June 14, 2016)

2016 ASMS user meeting presentations now online

We held two breakfast meetings in connection with the 64th ASMS Conference on Mass Spectrometry and Allied Topics in San Antonio, TX. If you were unable to attend, or want to review any of the material that was presented, you can find the slides and speaker notes here.

Posted by Web Master (May 18, 2016)

Mascot Distiller 2.6 released

We are pleased to announce the release of Mascot Distiller 2.6. Important new features include
  • Support for Waters MSE data, including quantitation
  • Reporter ion quantitation (iTRAQ and TMT) using MS3 scans
  • Summing or merging scans together according to scan type
  • Sciex ClearCore library for much faster peak picking of Wiff files
  • Searching peaklists using different ions series depending on the scan type
  • Entirely revised set of default processing options files

You can download Mascot Distiller from a link on the support page. If you wish to evaluate Mascot Distiller, send an email request to for a product key that can be registered on-line to obtain a 30 day licence. Without a licence, Distiller operates in viewer mode.